Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing

Analysis of the bacterial diversity in Moroccan Jben cheese using TTGE, DGGE, and 16S rRNA sequencing

This research investigated the physicochemical, microbiological, and bacterial diversity of Jben cheese, a popular artisanal variety in Morocco. The bacterial diversity was explored using culture-independent methods, including temporal temperature gel electrophoresis (TTGE), denaturing gradient gel electrophoresis (DGGE), and high-throughput sequencing (HTS). Significant intra-sample differences were observed for most physicochemical parameters within each milk type, while inter-sample differences occurred between cow and goat cheeses for dry matter and ash. Jben cheese exhibited distinct characteristics, with low pH values of 3.96, 4.16, and 4.18 for cow, goat, and mixed cheeses, respectively. Goat cheeses had higher fat (49.23 g/100 g), ash (1.91 g/100 g), and dry matter (36.39 g/100 g) than cow cheeses. All cheeses displayed high microbial counts, with a notable prevalence of the lactic acid bacteria (LAB) group, averaging 8.80 ± 0.92 log CFU/g. Jben cheese also displayed high contamination levels with total coliforms, faecal coliforms, yeast, and molds. Fatty acid profiling revealed fraudulent practices in Jben cheese marketing, with cow or mixed cheeses sold as goat cheese, as proven by low capric acid concentration. HTS analysis of Jben cheese identified ten genera and twenty-four species, highlighting Lactococcus lactis as predominant. TTGE and DGGE confirmed the presence of L. lactis but failed to provide the detailed profile achieved through HTS analysis. HTS has been demonstrated to be more reliable, whereas TTGE/DGGE methods, though informative, were more time-consuming and less reliable. Despite limitations, the combined use of TTGE, DGGE, and HTS provided a comprehensive view of indigenous bacterial communities in Jben cheese, identifying L. lactis as the main species.

Microbiome composition of kombucha tea from Türkiye using high-throughput sequencing

Kombucha is a fermented tea with a combination of yeast and bacteria. Kombucha teas may have a variable microbiota based on geographic origin and cultural conditions. The microbial flora of kombucha has been studied with culture-dependent methods. But, the improvement of the metataxonomic approach has broadened our perspective on fermented foods. In this study, a kombucha mother was procured from an artisanal supplier in Türkiye. High-throughput new-generation sequencing (16S rRNA and Internal Transcribed Spacer (ITS)) was carried out to investigate the microbial communities of kombucha after 7 days of fermentation in both liquid tea (L) and pellicle (P). Microbial counts, pH (4.42 ± 0.01 and 3.50 ± 0.02), and TA% (0.26 ± 0.02 and 0.60 ± 0.04) were also detected on the first and 7th days of fermentation. According to metataxonomic results, the dominant bacteria were Komagataeibacter obediens (%21.13), an acetic acid-producing bacteria, and the dominant fungal genus was Pichia kudriavzevii (64.35%) in L while Romboutsia sp. CE17 was the dominant bacteria (7%) and Pichia kudriavzevii was also the dominant yeast in P. This study also revealed different species which were not common in kombucha including propionic acid and butyric acid-producing bacteria such as Anaerotignum propionicum and Butyrivibrio fibrisolvens, a butyrivibriocin producing bacteria. Accordingly, different yeast species were detected such as Tetrapisispora phaffii and Ogataea polimorpha.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05725-z.

Metataxonomic sequencing to assess microbial safety of Turkish white cheeses

High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.

Approaching the sensory profile of Paipa cheese, the Colombian ripened cheese with protected designation of origin

Abstract Paipa cheese is the unique Colombian ripened cheese produced from raw milk that has a protected designation of origin (PDO); nonetheless, to date, the dairy product lacks a defined sensory profile, since no study has been previously performed. The aim of this study was to approach the definition of the sensory attributes of the Paipa cheeses that are produced within the PDO region in order to establish the organoleptic aspects of the PDO regulation. A trained panel of five members used the multidimensional approach as a descriptive sensory analysis to establish the sensory profile of Paipa cheese; such analysis was complemented with the method used for PDO cheeses were three cheese producers, two government delegates, one gastronomy expert and two Paipa cheese researchers participated in the descriptive sensory analysis. A microbiological assessment (mesophilic aerobic bacteria, lactic acid bacteria, total and fecal coliforms, coagulase-positive Staphylococci, Salmonella spp. and Listeria monocytogenes) of cheese samples was carried out prior to sensory analysis to guarantee the safety of the samples. The descriptive sensory analysis was performed with 17 cheese samples that represented 77% of Paipa cheese produced in the PDO region. 82 sensory descriptors were identified and 47 were finally established (seven descriptors for appearance, 15 for odor, 15 for taste and 10 for texture) for describing the sensory profile of Paipa cheese. Due to the presence of pathogenic bacteria, the texture and taste profiles of Paipa cheese were based only on three samples. Sensory profiles of cheese samples were highly heterogeneous and it may be a consequence of the variations among raw milk used and/or manufacturing practices of cheese producers. Therefore, in order to find the sensory identity of Paipa cheese and guarantee quality and safety, cheese production and raw milk characteristics must be defined and regulated among milk and Paipa cheese producers.

Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria monocytogenes

High throughput sequencing could become a powerful tool in food safety. This study was the first to investigate artisanal cheeses from Belgium (31 batches) using metagenetics, in relation to Listeria monocytogenes growth data acquired during a previous project. Five cheese types were considered, namely unripened acid-curd cheeses, smear- and mold-ripened soft cheeses, and Gouda-type and Saint-Paulin-type cheeses. Each batch was analyzed in triplicate the first and the last days of storage at 8 °C. Globally, 2697 OTUs belonging to 277 genera and to 15 phyla were identified. Lactococcus was dominant in all types, but Streptococcus was co-dominant in smear-ripened soft cheeses and Saint-Paulin-type cheeses. The dominant population was not always associated with added starter cultures. Bacterial richness and diversity were significantly higher in both types of soft cheeses than in other categories, including particular genera like Prevotella, Faecalibacterium and Hafnia-Obesumbacterium in mold-ripened cheeses and Brevibacterium, Brachybacterium, Microbacterium, Bacteroides, Corynebacterium, Marinilactibacillus, Fusobacterium, Halomonas and Psychrobacter in smear-ripened soft cheeses. A strong correlation was observed between no growth of L. monocytogenes in a smear-ripened cheese and the presence of an unknown Fusobacterium (relative abundance around 10%). This in silico correlation should be confirmed by further experiments in vitro and in situ.

Feasibility of Using Carvacrol/Starch Edible Coatings to Improve the Quality of Paipa Cheese

Paipa cheese is the only Colombian semi-ripened cheese with protected geographical indication. In the current work, the effect of applying starch coatings carrying carvacrol on Paipa cheeses was analyzed. Coatings were prepared based on blends of potato starch (2 g/100 g), carvacrol (0.1 g/100 g), polysorbate 80, glycerol, and water and applied to the cheese's surface by brushing. Uncoated cheeses were also analyzed for comparison. Moreover, films were prepared and characterized in terms of their moisture content, water vapor permeability, mechanical properties, transparency, water solubility, swelling (%), and antioxidant activity. Carvacrol/starch films showed a slight decrease in their water solubility and Young's modulus, while not significant changes were observed in water vapor permeability, moisture content, transparency, and swelling behavior, in comparison with the starch films. After application on the Paipa cheeses, the carvacrol/starch coatings enhanced the brightness of the cheeses without causing significant changes in water activity, moisture content, color attributes, and mesophilic aerobic bacteria and molds/yeasts count. Moreover, edible coatings have a significant effect on the hardness, the gumminess, the springiness, and the chewiness of the Paipa cheese. Coated cheeses were better preserved at day 60 of storage because they did not show changes in their lightness, hardness, and springiness.

Impact of DNA extraction methods on 16S rRNA-based profiling of bacterial communities in cheese

Numerous factors associated with sample preparation, DNA extraction, primer choice, sequencing platform and data analysis can affect the accuracy of 16S rRNA sequencing results. The DNA extraction method is considered critical for the success of sequencing as it can be the source of considerable variations in the analysis of the microbiome. In this study, the impact of various DNA extraction methods on the results of analysis of bacterial communities in cheese was evaluated. DNA was isolated from Mozzarella as a model cheese using optimized bead-based homogenization followed by different extraction procedures. Five commercial kits and two open-formula DNA extraction protocols were evaluated for amplicon sequencing of a 16S rRNA fragment of ~1460 bp. In addition, model cheese samples artificially contaminated by defined concentrations of Listeria monocytogenes and Escherichia coli, as representatives of Gram positive and Gram negative bacteria, were analysed. Six out of seven DNA extraction procedures were found to be able to provide amplifiable bacterial DNA suitable for 16S rRNA sequence analysis, but individual extraction procedures led to variable results. In particular, lysis supported with bead-beating led to a higher proportion of G+ bacteria in relative abundance profiles, probably because of the more efficient cell wall disruption. Artificially added bacterial species were reliably detected with a quantitative response. The results demonstrated a risk in comparing the data on bacterial communities in cheese when different DNA extraction protocols are used and highlighted the need to choose a standardized approach when comparison across multiple sequencing runs is required.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.